RetrogeneDB ID: retro_ocun_823

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 15:21946349..21946878(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000005906
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BAG2
• Ensembl ID: ENSOCUG00000004815
• Aliases: None
• Description: BCL2-associated athanogene 2 [Source:HGNC Symbol;Acc:938]

Sequence

>retro_ocun_823
ATGGCTTGGGTAAATATTAACGCCAAAGCCAATGAGGGACGCTTCTGGCGCTCCTCCTCCATGTCCAACCACTCCAGCTG
CTTGCTGGAGAGTCTGGACCAGCTGGCGCTCAGGGTTGAGGCTTTGAAAGAAGCAGCCAGTGCTGCTGAGCAAAAGAAGG
AAATTTTTCTGGAAATGATCCACAGTATCCATAATAGCCAGGACGTGAGGCAGATCAGCGATGGAGAAAGAGAATTAAAT
CTGACTGTGAACCCGCTTGATGGGACAAACCCTCACTGTTGGAGTTTCAGTAGAAACAATTAGAAATCCACAGCATCCAG
AATCCCTAAAACATGCCACAAGGATTATTGAGGATGTGGTCAATAAGTTTCTAGATTATCTGGGAAATGTTCAGAGTCAT
TTAACGTCACTCTACAGTGCCTGCTCATCTGAGGTGCTACCAGGGCCAGTTGATCACAAATTTCAATCCATAGTAATCGG
CTGTGCTCTTGAAGATCAGAAGAAAATTAAGAGAAGATTAGAAACAGTG

Alignment

ORF - retro_ocun_823 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.12 %
• Parental protein coverage: 83.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAQAKINAKANEGRFCRSSSMADRSSRLLESLDQLELRWVEALREAASAVEQEKEILLEMIHSIQNSQDM
          MA...INAKANEGRF.RSSSM...SS.LLESLDQL.LR.VEAL.EAASA.EQ.KEI.LEMIHSI.NSQD.
Retrocopy MAWVNINAKANEGRFWRSSSMSNHSSCLLESLDQLALR-VEALKEAASAAEQKKEIFLEMIHSIHNSQDV

Parental  RQISDGEREELNLTAN-RLMGRTLTVEVSVETIRNPQQQESLKHATRIIDDVVNKFLDDLGNAKNHLMSL
          RQISDGERE.LNLT.N.RLMG.TLTV.VSVETIRNPQ..ESLKHATRII.DVVNKFLD.LGN...HL.SL
Retrocopy RQISDGERE-LNLTVN>RLMGQTLTVGVSVETIRNPQHPESLKHATRIIEDVVNKFLDYLGNVQSHLTSL

Parental  YSACSSEVPPGPVDQKFQSIVIGCALEDQKKIKRRLETL
          YSACSSEV.PGPVD.KFQSIVIGCALEDQKKIKRRLET.
Retrocopy YSACSSEVLPGPVDHKFQSIVIGCALEDQKKIKRRLETV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	7.67 RPM
SRP017611_kidney	0.00 RPM	1.11 RPM
SRP017611_liver	0.00 RPM	1.08 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_823 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_823 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_823 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000028759	1 retrocopy	retro_cfam_252,
Myotis lucifugus	ENSMLUG00000004055	1 retrocopy	retro_mluc_251,
Oryctolagus cuniculus	ENSOCUG00000004815	1 retrocopy	retro_ocun_823 ,
Procavia capensis	ENSPCAG00000011588	1 retrocopy	retro_pcap_295,